Closed appliedmicrobiologyresearch closed 1 year ago
Hi Helena, does it work if you leave out the useRec=T
? If so it's a problem specifically with the recombination element. Is your data loaded using loadCFML
or loadGubbins
?
Thanks for the fast reply. loadgubbins. Aha, useRec=F and something is happening. Is that the right option then?
Do you mean that it is running fine with useRec=F
? If so then the problem is indeed with recombination but it should be possible to run with useRec=T
if that's what you want. Did you do anything between loadGubbins
and bactdate
, maybe to root the tree?
Yes.... Burkrooted=initRoot(tBurkGub,d) r=roottotip(Burkrooted,d) ...
It's still failing with useRec=T though...
Could you try again with
Burkrooted=initRoot(tBurkGub,d,useRec=T)
Excellent, thanks, that seems to have fixed it :-)
Great. For the record, you also had the option to run bactdate
directly on the unrooted tree rather than use initRoot(...,useRec=T)
and the effect would be exactly the same.
Hi Xavier! I have a new issue with BactDating. I have installed the newest version (1.1.1), and I am running on a tree with 18 tips and a beautiful regression. But I get the above error always after: bactBurk5m_arc=bactdate(tree = Burkrooted,date = d,useRec=T,nbIts=5e6,showProgress=T) I was looking through older issues, and my Burkrooted$unrec are also all nice numbers 0.93-1.00. The data set is from 2003 onwards. Thanks, Helena